An increasing number of genes have been linked to Alzheimer disease (AD) over the past decade. Recently, two different polymorphisms of the alpha-2-macroglobulin gene, residing on chromosome 12, were suggested to be associated with sporadic AD. One of these polymorphisms is based on a pentanucleotide deletion, the other is based on a point mutation by changing the nucleotide A to G (and the amino acid isoleucine to valine in the corresponding protein). The product of this gene is alpha-2-macroglobulin, a pan-proteinase inhibitor occurring in many organs and tissues including the brain. Several studies have suggested that alpha-2-macroglobulin may have protective effect against the deposition of beta-amyloids and may stimulate their degradation. Beta-amyloids now are considered to be major pathogenic factors in the cascade of events that lead to brain destruction with resultant memory loss and other manifestations of AD. A third recently identified gene polymorphism that has been linked to AD involves a C to T nucleotide mutation in the cathepsin D gene; located on chromosome 11. This mutation results in an amino acid sequence change of the gene's protein product from alanine to valine. The T allele may be associated with increased protein expression (increased pro-cathepsin D secretion) and altered intracellular maturation. Cathepsin D is a major intracellular aspartyl protease present in the endosomal-lysosomal system and has been shown to be involved in the pathogenesis of AD disease. Despite a number of studies supporting an association of the three different gene mutations (possibly all related to protein processing) with AD, there is also contrary evidence in the literature and therefore the relationships remain controversial. During the past few years, we developed methods that are more practicable (PCR-SSCPs for the two alpha-2-macroglobulin mutations and PCR-SSCP and LightCycler methods for the detection of the cathepsin D mutation) than conventional PCR-RFLPs for the study of these gene polymorphisms. Using these methods, we recently completed screening of approximately 400 subjects including patients confirmed to have AD and their family members for the three gene polymorphisms. Based on the results, we are now in the process of analyzing if there is a relationship between these gene mutations and the risk of AD. Based on the results, we are now in the process of analyzing if there is a relationship between these gene mutations and the risk of AD. In contrast to the alpha-2-macroglobulin and cathepsin D gene mutations, the apolipoprotein 4 allele is a well-established risk factor for AD. We recently validated and implemented for routine use a fully automated, real-time ultrafast PCR method based on the LightCycler instrument for more reliable and cost-effective determination of the alleles of the apolipoprotein gene.